If the leader, Qassim al-Rimi, wasn't there, the US military believed it would find intelligence that would help lead to him, the official said, though the official cautioned that the mission was not greenlit based on whether it was thought Al-Rimi would be at the site.
US Central Command, which oversees forces in the region, and the Pentagon are strongly denying al-Rimi was an objective of the raid just over a week ago.
On Tuesday, Pentagon spokesman Capt. Jeff Davis said, "There was never any intention, hope, anticipation or plan that he would be part of this operation."
"It wasn't a high-value target mission," Col. John Thomas told CNN on Monday, referring to operations aimed at killing or capturing terrorist leaders.
Thomas added that there was no hard intelligence indicating a "high possibility" al-Rimi was at the compound on the night of the raid, saying that the Navy SEALs would have captured AQAP leaders, including al-Rimi, as part of the intelligence-gathering operation.
"Anyone found on site would have been taken," Thomas said.
A senior US military official, however, told CNN that al-Rimi was part of the decision making to plan the operation.
Al-Rimi was not captured or killed and has since released an audio message mentioning the raid and taunting President Donald Trump.
US Special Operations forces have been searching for Al-Rimi in Yemen for years and the US has knowledge of locations where he and other AQAP leaders are suspected to travel and operate. Al-Rimi, however, has continued to elude detection.
first reported that al-Rimi was a target of the raid.
The chance to take out such a pivotal member of al Qaeda may explain the large allocation of resources used in the mission.
The raid led to the first US combat death since Trump took office. The mission combined US Navy SEALs with significant air support, as well as support from UAE special forces. In addition to the death of Chief Petty Officer William "Ryan" Owens, several SEALs were injured.
An 8-year-old girl, who was the daughter of Anwar Al-Awlaki, a US-born cleric who directed attacks against the US, was killed in the raid; al-Awlaki was killed in 2011. The London-based NGO Reprieve and a Sanaa-based human rights worker told CNN that at least 23 civilians were killed in the attack.
The SEAL team was detected by AQAP fighters prior to reaching its objective leading to the intense firefight.
Following news of the raid, the military had said the goal of the mission was to gather intelligence on AQAP.
On Friday, the Pentagon released clips from an al Qaeda training video seized during the raid, but later pulled those clips back because they were years old.
Government officials had previously told CNN
plans for the raid had been in the works for months and that Trump greenlit the mission shortly after his inauguration.
The Pentagon said the battle resulted in the deaths of 14 al Qaeda fighters, including two AQAP leaders.
Since its formation in 2009, many observers have considered among the most dangerous if not the most dangerous branch of al Qaeda.
Al-Rimi reportedly became the head of AQAP following the drone strike killing of Nasir al-Wuhayshi in 2015.